Calcium in PDB 3hx4: Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium

The structure of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium, PDB code: 3hx4 was solved by A.K.Wernimont, J.D.Artz, P.Finnerty, T.Xiao, H.He, F.Mackenzie, G.Sinestera, A.A.Hassani, G.Wasney, M.Vedadi, S.Lourido, A.Bochkarev, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, D.L.Sibley, R.Hui, Y.H.Lin, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.236, 95.605, 101.612, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.7

The binding sites of Calcium atom in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium (pdb code 3hx4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium, PDB code: 3hx4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:32.0 occ:1.00 O A:TYR421 2.3 21.1 1.0 OD1 A:ASP415 2.3 26.1 1.0 OD1 A:ASP417 2.3 25.6 1.0 OE2 A:GLU423 2.4 27.2 1.0 OE1 A:GLU426 2.4 21.4 1.0 OD1 A:ASN419 2.4 20.3 1.0 OE2 A:GLU426 2.6 22.3 1.0 CD A:GLU426 2.9 22.2 1.0 CG A:ASN419 3.4 22.7 1.0 CG A:ASP415 3.4 26.5 1.0 CD A:GLU423 3.5 29.2 1.0 CG A:ASP417 3.5 26.7 1.0 C A:TYR421 3.5 20.7 1.0 OE1 A:GLU423 3.9 29.4 1.0 ND2 A:ASN419 4.0 21.0 1.0 OD2 A:ASP417 4.0 26.7 1.0 OD2 A:ASP415 4.1 25.9 1.0 N A:ASN419 4.3 23.6 1.0 CA A:ASP415 4.3 26.9 1.0 N A:TYR421 4.3 21.9 1.0 N A:GLU423 4.3 20.3 1.0 N A:ASP417 4.3 26.1 1.0 CG A:GLU426 4.3 21.3 1.0 CB A:ASP415 4.4 26.4 1.0 N A:ILE422 4.4 20.5 1.0 CA A:ILE422 4.4 20.3 1.0 CB A:ASN419 4.4 22.9 1.0 CA A:TYR421 4.4 21.0 1.0 C A:ASP415 4.5 26.5 1.0 N A:PHE416 4.6 26.7 1.0 N A:LYS418 4.7 25.3 1.0 CB A:ASP417 4.7 26.0 1.0 CG A:GLU423 4.7 24.6 1.0 CA A:ASN419 4.7 23.3 1.0 CB A:GLU423 4.8 21.5 1.0 C A:ILE422 4.8 20.6 1.0 CB A:TYR421 4.8 20.6 1.0 CA A:ASP417 4.8 26.2 1.0 N A:GLY420 4.9 22.9 1.0 C A:ASP417 4.9 25.8 1.0 O A:HOH541 4.9 16.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:31.9 occ:1.00 OD1 A:ASP368 2.2 24.3 1.0 O A:HOH508 2.2 21.4 1.0 O A:GLN374 2.3 25.3 1.0 OD1 A:ASN370 2.3 22.1 1.0 OE1 A:GLU379 2.4 21.6 1.0 OD2 A:ASP372 2.4 19.5 1.0 OE2 A:GLU379 2.5 19.1 1.0 CD A:GLU379 2.8 21.3 1.0 CG A:ASN370 3.4 23.7 1.0 CG A:ASP372 3.4 22.1 1.0 CG A:ASP368 3.4 23.3 1.0 C A:GLN374 3.5 25.7 1.0 OD1 A:ASP372 3.8 22.7 1.0 ND2 A:ASN370 3.8 21.9 1.0 N A:GLN374 4.1 26.2 1.0 OD2 A:ASP368 4.2 23.0 1.0 N A:ASP372 4.2 22.1 1.0 CG A:GLU379 4.3 22.4 1.0 CA A:GLN374 4.3 26.2 1.0 CA A:ASP368 4.4 23.0 1.0 CB A:ASP368 4.4 22.9 1.0 N A:ASN370 4.4 23.4 1.0 N A:LEU375 4.4 24.6 1.0 CA A:LEU375 4.4 24.1 1.0 N A:GLY371 4.5 23.2 1.0 C A:ASP368 4.5 23.1 1.0 CB A:ASP372 4.6 22.6 1.0 N A:ASP376 4.6 23.8 1.0 CB A:GLN374 4.6 26.9 1.0 CB A:ASN370 4.6 23.2 1.0 N A:GLY373 4.7 24.0 1.0 N A:LYS369 4.7 23.4 1.0 OD2 A:ASP376 4.8 25.8 1.0 CA A:ASP372 4.8 22.8 1.0 CA A:ASN370 4.8 23.6 1.0 C A:ASN370 4.9 23.5 1.0 C A:ASP372 4.9 23.2 1.0 C A:LEU375 5.0 24.4 1.0 CG A:ASP376 5.0 24.4 1.0 O A:ASP368 5.0 22.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:47.7 occ:1.00 O A:HOH587 2.2 25.5 1.0 OD1 A:ASP451 2.2 23.0 1.0 O A:LYS457 2.3 24.3 1.0 OD2 A:ASP453 2.4 28.0 1.0 OG A:SER455 2.5 25.3 1.0 OE2 A:GLU462 2.6 27.9 1.0 OE1 A:GLU462 2.7 25.1 1.0 CD A:GLU462 3.0 26.3 1.0 CG A:ASP451 3.4 23.8 1.0 CG A:ASP453 3.5 27.5 1.0 C A:LYS457 3.5 24.1 1.0 CB A:SER455 3.6 26.7 1.0 OD1 A:ASP453 3.9 26.6 1.0 N A:SER455 3.9 26.9 1.0 N A:LYS457 4.1 24.4 1.0 CA A:ASP451 4.2 24.9 1.0 CA A:SER455 4.3 26.4 1.0 OD2 A:ASP451 4.3 21.9 1.0 CB A:ASP451 4.3 24.2 1.0 N A:ILE458 4.4 23.6 1.0 CA A:LYS457 4.4 24.2 1.0 C A:ASP451 4.4 24.9 1.0 CA A:ILE458 4.4 23.0 1.0 N A:ASP453 4.5 26.6 1.0 CG A:GLU462 4.5 25.5 1.0 N A:ASN454 4.6 27.3 1.0 N A:SER452 4.6 25.6 1.0 N A:GLY456 4.6 25.7 1.0 CB A:ASP453 4.7 26.8 1.0 N A:SER459 4.8 22.6 1.0 C A:SER455 4.8 26.2 1.0 C A:ASP453 4.8 26.9 1.0 CA A:ASP453 4.9 26.9 1.0 O A:ASP451 4.9 25.1 1.0 C A:ASN454 5.0 27.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:49.2 occ:1.00 O A:HOH588 2.2 19.8 1.0 O A:GLU491 2.4 24.6 1.0 OD2 A:ASP485 2.4 27.7 1.0 OD1 A:ASN487 2.4 24.5 1.0 OE1 A:GLU496 2.5 26.0 1.0 OE2 A:GLU496 2.6 25.4 1.0 OD1 A:ASP489 2.6 26.5 1.0 CD A:GLU496 2.9 24.9 1.0 CG A:ASP489 3.3 26.7 1.0 CG A:ASP485 3.6 26.9 1.0 C A:GLU491 3.6 24.6 1.0 OD2 A:ASP489 3.6 27.2 1.0 CG A:ASN487 3.6 27.0 1.0 OD2 A:ASP493 4.2 26.2 1.0 ND2 A:ASN487 4.2 26.8 1.0 N A:GLU491 4.2 24.5 1.0 N A:ASP489 4.3 26.0 1.0 OD1 A:ASP485 4.3 26.2 1.0 CA A:ASP485 4.3 27.3 1.0 CG A:GLU496 4.4 24.6 1.0 N A:VAL492 4.5 24.4 1.0 CA A:VAL492 4.5 24.0 1.0 N A:ASN487 4.5 27.0 1.0 CA A:GLU491 4.5 25.0 1.0 CB A:ASP485 4.5 27.2 1.0 N A:ASP493 4.5 24.6 1.0 CB A:ASP489 4.6 25.9 1.0 N A:ASN488 4.6 26.3 1.0 C A:ASP485 4.7 27.4 1.0 N A:LYS486 4.7 27.4 1.0 CB A:ASN487 4.7 26.8 1.0 N A:GLY490 4.8 25.2 1.0 CA A:ASP489 4.8 25.8 1.0 C A:ASN487 4.8 26.6 1.0 CG A:ASP493 4.8 25.6 1.0 CA A:ASN487 4.9 26.9 1.0

A.K.Wernimont, J.D.Artz, P.Finerty, Y.H.Lin, M.Amani, A.Allali-Hassani, G.Senisterra, M.Vedadi, W.Tempel, F.Mackenzie, I.Chau, S.Lourido, L.D.Sibley, R.Hui. Structures of Apicomplexan Calcium-Dependent Protein Kinases Reveal Mechanism of Activation By Calcium. Nat.Struct.Mol.Biol. V. 17 596 2010.
ISSN: ISSN 1545-9993
PubMed: 20436473
DOI: 10.1038/NSMB.1795